BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716675.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,001,486 number of mapped reads = 1,837,085 (91.79%) number of supplementary alignments = 9,857 (0.49%) number of secondary alignments = 0 number of mapped bases = 107,226,255 bp number of sequenced bases = 107,197,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,974 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.791 >>>>>>> ACTG content number of A's = 25,780,194 bp (24.05%) number of C's = 19,571,187 bp (18.26%) number of T's = 34,831,841 bp (32.49%) number of G's = 27,013,872 bp (25.2%) number of N's = 657 bp (0%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 528,801 number of insertions = 7,366 mapped reads with insertion percentage = 0.4% number of deletions = 18,317 mapped reads with deletion percentage = 0.99% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.2974X There is a 3.05% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13182564 0.05288879099723487 0.5020488480737252 chr2 243199373 10811470 0.044455172176780244 0.4288304686395679 chr3 198022430 7039103 0.03554699838801089 0.2089833658222688 chr4 191154276 4476118 0.023416258812855435 0.18801510669846574 chr5 180915260 7891030 0.04361727142309609 0.23202455043864 chr6 171115067 4092116 0.023914410763138702 0.20087844368392868 chr7 159138663 6857761 0.04309299117336433 0.4370541847036034 chr8 146364022 4800806 0.03280045146613968 0.26710571192578014 chr9 141213431 2847410 0.02016387520532661 0.22302889203183218 chr10 135534747 4614744 0.034048420070463555 0.25165559219556405 chr11 135006516 4520140 0.03348090250695752 0.2737192874280203 chr12 133851895 4259214 0.03182034890129871 0.2001724014716216 chr13 115169878 3049125 0.0264750215329741 0.18231110926141017 chr14 107349540 2229858 0.02077193810052656 0.16831844668621856 chr15 102531392 4702897 0.045867874299414566 0.23838160714537773 chr16 90354753 3309981 0.03663316970165366 0.22583316393278932 chr17 81195210 3971927 0.04891824283723141 0.26441165515510084 chr18 78077248 3444994 0.04412289224128391 0.4794203394477659 chr19 59128983 1636549 0.02767761116405469 0.3563689318339152 chr20 63025520 2603373 0.041306648481440535 0.22871715604198017 chr21 48129895 1323460 0.027497670626540946 0.1903198459384357 chr22 51304566 1308618 0.025506852547977892 0.17730094304118302 chrMT 16571 5466 0.32985335827650714 0.6043313510488229 chrX 155270560 4009131 0.02582029072349581 0.2031284032844838 chrY 59373566 238400 0.004015254869481817 0.09163459816406586